DESCRIPTION

 Package: shinyscreen
 Title: Pre-screening of Mass Spectrometry Data 
-Version: 0.8
+Version: 0.9.0
 Author: Todor Kondić
 Maintainer: Todor Kondić <todor.kondic@uni.lu>
 Authors@R: 
@@ -29,7 +29,7 @@ Description: Pre-screening of Mass Spectrometry Data.
 License: Apache License (>= 2.0)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
 Roxygen: list(markdown = TRUE)
 Collate:
     'resources.R'
@@ -37,7 +37,10 @@ Collate:
     'mix.R'
     'extraction.R'
     'run.R'
-    'shinyUI.R'
+    'api.R'
+    'shiny-ui-base.R'
+    'shiny-ui-config.R'
+    'shiny-ui-top.R'
 Depends:
     RMassBank,
     RChemMass
@@ -48,6 +51,9 @@ Imports:
     yaml,
     mzR,
     MSnbase,
+    data.table,
+    assertthat,
+    withr,
     ggplot2,
     cowplot,
     RColorBrewer,

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
+export(gen)
+export(gen_base_ftab)
 export(launch)
+export(load_inputs)
+export(mk_comp_tab)
+export(read_conf)
+export(run)
+export(run_in_dir)
+export(vrfy_conf)
+import(data.table)
+importFrom("(shiny,","validate)")

R/api.R

+## Copyright (C) 2020 by University of Luxembourg
+
+## Licensed under the Apache License, Version 2.0 (the "License");
+## you may not use this file except in compliance with the License.
+## You may obtain a copy of the License at
+
+##     http://www.apache.org/licenses/LICENSE-2.0
+
+## Unless required by applicable law or agreed to in writing, software
+## distributed under the License is distributed on an "AS IS" BASIS,
+## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+## See the License for the specific language governing permissions and
+## limitations under the License.
+
+
+##' @export
+run <- function(fn_conf) {
+    conf <- read_conf(fn_conf)
+    dir.create(conf$project,
+               showWarnings = F,
+               recursive = T)
+    
+    withr::with_dir(new=conf$project,code = run_in_dir(conf))
+    return()
+}
+
+
+##' @export
+run_in_dir <- function(conf) {
+    m <- load_inputs(conf)
+    m <- mk_comp_tab(m)
+    m <- gen_base_tab(m)
+    stop()
+    m
+    
+}
+
+##' @export
+gen_base_ftab <- function(m) {
+    files <- add_wd_to_mzml(df=m$input$tab$mzml,wdir=m$conf$project)
+    df <- gen_sup_ftab(files,m$out$tab$comp)
+    tab2file(df,file.path(m$conf$project,FN_FTAB_BASE))
+    m$out$tab$ftab <- df
+}
+
+##' @export
+load_inputs <- function(conf) {
+    m<-list()
+    m$conf <- conf
+    m$input$tab$mzml <- file2tab(m$conf$data)
+    m$input$tab$known <- if (shiny::isTruthy(m$input$tab$known))
+                             file2tab(m$conf$compounds$known) else EMPTY_KNOWN
+    m$input$tab$unknown <- if (shiny::isTruthy(m$input$tab$unknown))
+                               file2tab(m$conf$compounds$unknown) else EMPTY_UNK
+    m$input$tab$setid <- read_setid(m$conf$compounds$sets,
+                                    m$input$tab$known,
+                                    m$input$tab$unknown)
+    m
+}
+
+##' @export
+mk_comp_tab <- function(m) {
+    message("Started assembling the lists of knowns and unknowns into the `comprehensive' table.")
+    setid <- m$input$tab$setid
+    setkey(setid,set,ID)
+    mzml<- m$input$tab$mzml
+    setkey(mzml,set)
+    
+    unk<-m$input$tab$unknown
+    setkey(unk,ID)
+    known<-m$input$tab$known
+    setkey(known,ID)
+    assertthat::assert_that(xor(nrow(unk)==0,nrow(known)==0),msg="No compound lists have been provided. At least one of the known, or unknown compound lists is required.")
+    message("Begin generation of comp table.")
+    ## knowns
+    setidKnown<- merge(mzml[,.(mode,set)],setid[origin=="known",],allow.cartesian = T)
+    compKnown <- setidKnown[known,on="ID"]
+    compKnown[,`:=`(mz=mapply(get_mz_from_smiles,SMILES,mode,USE.NAMES = F))]
+    message("Generation of comp table: knowns done.")
+
+    ## unknows
+    setidUnk<-merge(mzml[,.(mode,set)],setid[origin=="unknown",],allow.cartesian = T)
+    compUnk <- setidUnk[unk,on="ID"]
+    message("Generation of comp table: unknowns done.")
+    df<-rbindlist(l=list(compKnown, compUnk),fill = T)
+    setnames(df,names(COMP_NAME_MAP),
+             function(o) COMP_NAME_MAP[[o]])
+    fn_out <- file.path(m$conf$project,FN_COMP_TAB)
+    
+    tab2file(tab=df,file=fn_out)
+    message("Generation of comp table finished.")
+    setkeyv(df,c("set","tag","mz"))
+    m$out$tab$comp <- df
+    m
+}
+
+##' @export
+read_conf <- function(fn_conf) {
+    assertthat::assert_that(file.exists(fn_conf),msg=paste("Unable to read the configuration file:", fn_conf))
+    conf <- yaml::yaml.load_file(fn_conf)
+    conf <- vrfy_conf(conf)
+    conf
+}
+
+##' @export
+vrfy_conf <- function(conf) {
+    ## * Existence of input files
+
+
+
+    fn_cmpd_known <- conf$compounds$known
+    fn_cmpd_unk <- conf$compounds$unknown
+    fn_cmpd_sets <- conf$compounds$sets
+
+    ## ** Compound lists and sets
+
+    assertthat::assert_that(file.exists(fn_cmpd_sets),
+                            msg=paste("Cannot find the compound sets file:",fn_cmpd_sets))
+    
+    if (!is.null(fn_cmpd_known)) assertthat::assert_that(file.exists(fn_cmpd_known),
+                                                             msg=paste("Cannot find known compounds file:",fn_cmpd_known))        
+    if (!is.null(fn_cmpd_unk)) assertthat::assert_that(file.exists(fn_cmpd_unk),
+                                                       msg=paste("Cannot find unknown compounds file:",fn_cmpd_unk))
+
+
+    ## * Data files
+    df_sets <- file2tab(fn_cmpd_sets)
+    all_sets<-unique(df_sets$set)
+
+    fn_data <- conf$data
+    assertthat::assert_that(file.exists(fn_data),msg=paste("Data table does not exist:",fn_data))
+    mzml <- file2tab(fn_data)
+    
+    no_files <- which(mzml[,!file.exists(Files)])
+    no_modes <- which(mzml[,!(mode %in% names(MODEMAP))])
+    no_sets <- which(mzml[,!(set %in% all_sets)])
+    assertthat::assert_that(length(no_files)==0,msg = paste("Non-existent data files at rows:",paste(no_files,collapse = ','), "of",fn_data))
+    assertthat::assert_that(length(no_modes)==0,msg = paste("Unrecognised modes at rows:",paste(no_modes,collapse = ','), "of", fn_data))
+    assertthat::assert_that(length(no_sets)==0,msg = paste("Unknown sets at rows:",paste(no_sets,collapse = ','),"of", fn_data))
+
+    df_k <- file2tab(fn_cmpd_known)
+    
+    are_knowns_OK <- shiny::isTruthy(vald_comp_tab(df_k,fn_cmpd_known, checkSMILES=T, checkNames=T))
+    assertthat::assert_that(are_knowns_OK)
+
+    ## ** Unknowns
+    if (!is.null(fn_cmpd_unk)) {
+        df_u <- file2tab(fn_cmpd_unk)
+        are_unknowns_OK <- shiny::isTruthy(vald_comp_tab(df_u,fn_cmpd_unk, checkSMILES=F, checkMz=T))
+        assertthat::assert_that(are_unknowns_OK)
+    }
+    
+    
+    
+    return(conf)
+}
+
+

R/base.R

@@ -12,16 +12,18 @@
 ## See the License for the specific language governing permissions and
 ## limitations under the License.
 
+
+##' @import data.table
+## Redirections
+the_ifelse <- data.table::fifelse
+dtable <- data.table::data.table
+
 tab2file<-function(tab,file,...) {
-    write.csv(x=tab,file=file,row.names=F,...)
+    data.table::fwrite(x=tab,file=file,...)
 }
 
-file2tab<-function(file,stringsAsFactors=F,comment.char='',sep=',',...) {
-    read.csv(file=file,
-             header=T,
-             stringsAsFactors=stringsAsFactors,
-             comment.char=comment.char,
-             na.strings=c("","NA"),...)
+file2tab<-function(file,na.strings=c("","NA"),...) {
+    data.table::fread(file=file,na.strings = na.strings, ...)
 }
 
 isThingFile<-function(fn) {
@@ -30,3 +32,13 @@ isThingFile<-function(fn) {
     } else F
 }
 
+## Stolen from Stack Overflow
+split_path <- function(path) {
+  if (dirname(path) %in% c(".", path)) return(basename(path))
+  return(c(basename(path), split_path(dirname(path))))
+}
+
+
+print_table <- function (df) {
+    paste(apply(df,1,function (row) paste(row,collapse=',')),collapse = "\n")
+}

R/extraction.R

@@ -267,20 +267,6 @@ gen_ms1_chrom_ht<-function(raw,mz,errEIC,rt=NULL,errRT=NULL) {
     res
 }
 
-
-
-tab2file<-function(tab,file,...) {
-    write.csv(x=tab,file=file,row.names=F,...)
-}
-
-file2tab<-function(file,stringsAsFactors=F,comment.char='',...) {
-    read.csv(file=file,
-             header=T,
-             stringsAsFactors=stringsAsFactors,
-             comment.char=comment.char,
-             na.strings=c("","NA"),...)
-}
-
 get_ext_width <- function(maxid) {as.integer(log10(maxid)+1)}
 id_fn_ext<-function(width,id) {
     formatC(as.numeric(id),width=width,flag=0)

R/mix.R

@@ -31,6 +31,10 @@ get_mz_cmp_l<-function(id,mode,cmpL) {
     res
 }
 
+get_mz_from_smiles <- function(smiles,mode) {
+    RChemMass::getSuspectFormulaMass(smiles)[[MODEMAP[[mode]]]]
+}
+
 get_col_from_cmp_l<-function(id,cname,cmpL) {
     ind<-match(id,cmpL$ID)
     x<-cmpL[[cname]][[ind]]
@@ -53,7 +57,7 @@ pp_touch_q<-function(ftab) {
     which(ftab$checked==FTAB_CHK_NONE | ftab$checked==FTAB_CHK_AUTO)
 }
 
-preProc <- function (ftable,noiseFac=3,errRT=0.5,intThreshMS1=1e5,intThreshMS2=0.05) {
+preProc <- function (ftable,noiseFac=3,errRT=0.5,intThreshMS1=1e5,intThreshMS2=5000.) {
     wds<-unique(ftable$wd)
     fn_spec<-function(wd) readRDS(file.path(wd,FN_SPEC))
     message("Loading RDS-es ...")
@@ -145,7 +149,7 @@ preProc <- function (ftable,noiseFac=3,errRT=0.5,intThreshMS1=1e5,intThreshMS2=0
                 eicFilt<- eic[rtIndMS1,]
                 eicFilt<- eicFilt[which(eicFilt$intensity>intThreshMS1),]
                 mInt<- maxInt #mean(eicFilt$intensity)
-                rtInd <- rtInd[which(msms$intensity[rtInd]>intThreshMS2*mInt)] #Intense enough?
+                rtInd <- rtInd[which(msms$intensity[rtInd]>intThreshMS2)] #Intense enough?
                 msmsRT <- msms$rt[rtInd]
                 msmsInt<- msms$intensity[rtInd]
                 if (length(msmsRT) > 0) {
@@ -449,7 +453,7 @@ plot_id_msn <- function(ni,
 
 
 
-adornmzMLTab<-function(df,projDir=getwd()) {
+add_wd_to_mzml <- function(df,wdir) {
     pref<-df$set
     mask<-is.na(pref)
     drop<-df$files[mask]
@@ -457,36 +461,16 @@ adornmzMLTab<-function(df,projDir=getwd()) {
     df<-df[!mask,]
     pref<-df$set
     wd<-basename(tools::file_path_sans_ext(df$Files))
-    wd<-file.path(projDir,pref,wd)
+    wd<-file.path(wdir,pref,wd)
     df$wd<-wd
     df
 }
 
-genSuprFileTab <- function(fileTab,compTab) {
-    genOne<-function(ids,fn) {
-
-        K<-length(ids)
-        fTabRow<-fileTab[fileTab$Files == fn,]
-        cols<-lapply(names(fileTab),function(n) rep(fTabRow[[n]],K))
-        names(cols)<-NULL
-        cols<-c(cols,list(ids))
-        names(cols)<-c(names(fileTab),"ID")
-        df<-as.data.frame(cols,stringsAsFactors = F)
-        df
-    }
-    
-    tabs<-lapply(fileTab$Files,function(fn)
-    {
-        wh<-which(fileTab$Files==fn)
-        set<-fileTab$set[[wh]]
-        md<-fileTab$mode[[wh]]
-        sel<-(compTab$set %in% set) & (compTab$mode %in% md)
-        ids<-compTab$ID[sel]
-        genOne(ids,fn)
-        
-    })
-    res<-do.call(rbind,tabs)
-    res
+gen_sup_ftab <- function(ftab,ctab) {
+    df<-ctab[ftab,on=c("set","mode"),allow.cartesian=T]
+    setkeyv(df,cols=FTAB_KEY)
+    setcolorder(df,neworder = FTAB_NAMES)
+    df
 }
 
 getEntryFromComp<-function(entry,id,set,mode,compTab) {
@@ -496,9 +480,13 @@ getEntryFromComp<-function(entry,id,set,mode,compTab) {
 
     res<- if (length(ind)==1) compTab[ind,entry] else {
                                                      if (length(ind)>1) {
-                                                         stop("Nonunique entry selection in comprehensive table.")
+                                                         warning("Nonunique selection in comprehensive table:")
+                                                         for (i in ind) {
+                                                             message('ID: ',compTab$ID[[i]],' set: ',compTab$set[[i]],' mode: ',compTab$mode[[i]])
+                                                         }
+                                                         warning("The compound set table likely containes duplicate IDs per set/mode combination. Please correct this.")
                                                      } else {
-                                                         stop("Entries not found for id ", id,"set ",set, "and mode ", mode, " .")
+                                                         warning("Entries not found for id ", id,"set ",set, "and mode ", mode, " .")
                                                      } 
                                                  }
     res
@@ -506,29 +494,32 @@ getEntryFromComp<-function(entry,id,set,mode,compTab) {
     res
         
 }
-addCompColsToFileTbl<-function(ft,compTab) {
-    nR<-nrow(ft)
-    mzCol<-rep(NA,nR)
-    nmCol<-rep("",nR)
-    rtCol<-rep(NA,nR)
+## add_comp_ftab <- function(ft,ctab) {
+##     nR<-nrow(ft)
+##     mzCol<-rep(NA,nR)
+##     nmCol<-rep("",nR)
+##     rtCol<-rep(NA,nR)
     
-    for (ir in 1:nR) {
-        id<-ft[ir,"ID"]
-        set<-ft[ir,"set"]
-        m<-ft[ir,"mode"]
-        entries<-getEntryFromComp(c("mz","Name","rt"),id,set,m,compTab)
-        mzCol[[ir]]<-  entries[["mz"]]
-        nm<-entries[["Name"]]
-        nmCol[[ir]]<- if (!is.na(nm)) nm else ""
-        rtCol[[ir]]<- entries[["rt"]]
-    }
-    ft$mz<-mzCol
-    ft$Name<-nmCol
-    ft$rt<-rtCol
-    ft
+##     for (ir in 1:nR) {
+##         id<-ft[ir,"ID"]
+##         set<-ft[ir,"set"]
+##         m<-ft[ir,"mode"]
+##         entries<-getEntryFromComp(c("mz","Name","rt"),id,set,m,ctab)
+##         mzCol[[ir]]<-  entries[["mz"]]
+##         nm<-entries[["Name"]]
+##         nmCol[[ir]]<- if (!is.na(nm)) nm else ""
+##         rtCol[[ir]]<- entries[["rt"]]
+##     }
+##     ft$mz<-mzCol
+##     ft$Name<-nmCol
+##     ft$rt<-rtCol
+##     ft
+## }
+
+get_set_mode <- function(s,mzml) {
+    unique(mzml[set == s,mode])
 }
 
-
 vald_comp_tab<-function(df,ndf,checkSMILES=F,checkMz=F,checkNames=F) {
     ## Fields.
     if (is.null(df$ID)) stop("Column ID missing in ",ndf," .")
@@ -574,7 +565,6 @@ vald_comp_tab<-function(df,ndf,checkSMILES=F,checkMz=F,checkNames=F) {
         ll<-length(unique(df$SMILES))
         if (ll<lsmiles) {
             warning("There are duplicate SMILES in the compound list. Trouble ahead.")
-            return(NULL)
         }
     }
 
@@ -591,3 +581,23 @@ vald_comp_tab<-function(df,ndf,checkSMILES=F,checkMz=F,checkNames=F) {
 
     df
 }
+
+read_setid <- function(fn,known,unk) {
+    setid <- file2tab(fn)
+    id_k <- known$ID
+    id_u <- unk$ID
+    tmp <- setid[,.(ID,set,origin=the_ifelse(ID %in% id_k,"known",NA_character_))]
+    tmp <- tmp[,.(ID,set,origin=the_ifelse(is.na(origin) & ID %in% id_u,"unknown",origin))]
+    natmp <- tmp[is.na(origin),.(ID,set)]
+    assertthat::assert_that(nrow(natmp)==0,msg=paste("The following IDs from set table have not been found in the compound table:","------",print_table(natmp),"------",sep = "\n"))
+    tmp
+}
+
+
+write_conf <- function(conf,fn) {
+    yaml::write_yaml(x=conf,file=fn)
+}
+
+read_conf <- function(fn) {
+    yaml::yaml.load_file(fn)
+}

R/resources.R

@@ -14,6 +14,14 @@
 
 
 
+
+## Config defaults
+CONF <- list(data=NA_character_,
+             project=getwd(),
+             compounds=list(known=NA_character_,
+                            unknown=NA_character_,
+                            sets=NA_character_))
+
 ## Constants
 FN_FTAB_BASE<-"ftable.base.csv"
 FN_FTAB_PP<-"ftable.pp.csv"
@@ -24,12 +32,12 @@ FN_CMP_L<-"compounds.csv"
 FN_LOC_SETID <-"setid.csv"
 FN_COMP_TAB<-"comprehensive.csv"
 FN_SPEC<-"specdata.rds"
-MODEMAP<-list(pH="MpHp_mass",
-              mH="MmHm_mass",
-              pNH4="MpNH4_mass",
-              pNa="MpNa_mass")
+MODEMAP<-list("[M+H]+"="MpHp_mass",
+              "[M-H]-"="MmHm_mass",
+              "[M+NH4]+"="MpNH4_mass",
+              "[M+Na]+"="MpNa_mass")
 
-TAG_DEF<-"unspecified"
+TAG_DEF <- "unspecified"
 TAG_DEF_DESC<-"Case"
 DEFAULT_RT_RANGE=c(NA,NA)
 DEFAULT_INT_RANGE=c(NA,NA)
@@ -90,7 +98,7 @@ RT_EXTR_ERR<-0.5                       # min
 RT_SHIFT_ERR <- 0.5               # min
 
 MS1_INT_THOLD <- 1e5
-MS2_INT_THOLD <- 0.05
+MS2_INT_THOLD <- 5000.
 
 MS1_SN_FAC <- 3.0
 
@@ -98,3 +106,15 @@ MS1_SN_FAC <- 3.0
 ## Shiny objects
 
 NUM_INP_WIDTH="15%"
+
+## Comprehensive table properties
+COMP_NAME_MAP <- list(RT="rt")
+# COMP_NAMES <-c("ID","mz","rt","mode","set","origin","Name","SMILES")
+
+## File table properties
+FTAB_KEY=c("set","tag","mz")
+FTAB_NAMES=c("ID", "mz", "rt", "tag", "mode", "set", "Name", "SMILES", "Files" , "wd","origin")
+
+
+EMPTY_UNK <- data.table(ID=character(0),mz=numeric(0),RT=numeric(0),Name=character(0),CAS=character(0))
+EMPTY_KNOWN <- data.table(ID=character(0),SMILES=character(0),RT=numeric(0),Name=character(0),CAS=character(0))

R/shiny-ui-base.R

+## Copyright (C) 2020 by University of Luxembourg
+
+## Licensed under the Apache License, Version 2.0 (the "License");
+## you may not use this file except in compliance with the License.
+## You may obtain a copy of the License at
+
+##     http://www.apache.org/licenses/LICENSE-2.0
+
+## Unless required by applicable law or agreed to in writing, software
+## distributed under the License is distributed on an "AS IS" BASIS,
+## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+## See the License for the specific language governing permissions and
+## limitations under the License.
+
+##' @importFrom(shiny, validate)
+
+react_v <- shiny::reactiveValues
+react_f <- shiny::reactive
+react_e <- shiny::eventReactive
+obsrv <- shiny::observe
+obsrv_e <- shiny::observeEvent
+vols <- shinyFiles::getVolumes
+vol_f <- vols()
+validate1 <- function(expr,msg) shiny::validate(need(expr,msg))
+
+
+path2vol <- function(path) {
+    ## This function returns shinyFiles compatible volumes.
+    splits <- split_path(path)
+    file.path(tail(splits,1),'')
+}
+
+
+prim_box<-function(...) {shinydashboard::box(...,
+                                             status="primary",
+                                             solidHeader=T)}
+good_box<-function(...) {shinydashboard::box(...,
+                                             status="success",
+                                             solidHeader=T)}
+err_box<-function(...) {shinydashboard::box(...,
+                                            status="danger",
+                                            solidHeader=T)}
+
+inact_box<-function(...) {shinydashboard::box(...,
+                                            status="danger",
+                                            solidHeader=T)}
+
+
+html<-function(...) {shiny::tags$div(shiny::HTML(...))}
+
+## num_input<-function(...,width=NUM_INP_WIDTH) {shiny::tags$div(id="inline",shiny::textInput(...,width=width))}
+
+num_input <- function(inputId,label,...,width=NUM_INP_WIDTH) {
+    shiny::tags$div(style="display:inline-block",
+                    shiny::tags$label(label, `for` = inputId),
+                    shiny::tags$input(id = inputId, type = "text",style=paste("width:",width,sep = ""),...))
+}
+num_input_unit <- function(inputId,l1,l2,width=NUM_INP_WIDTH,...) {
+    shiny::tags$div(style="display:inline-block",
+                    shiny::tags$label(l1, `for` = inputId), 
+                    shiny::tags$input(id = inputId, type = "text",style=paste("width:",width,sep = ""),...),
+                    shiny::tags$label(paste(" ",l2,sep=""), `for` = inputId))
+}
+
+txt_file_input <- function(inputId,input,fileB,label,volumes) {
+
+    fnobj<-shinyFiles::parseFilePaths(roots = volumes,
+                                      selection = input[[fileB]])
+    fn <- fnobj[['datapath']]
+    
+    if (isThingFile(fn)) {
+        shiny::textInput(inputId = inputId,
+                         label = label,
+                         value = fn)
+    } else {
+        shiny::isolate(currFn <- input[[inputId]])
+        if (!isThingFile(currFn)) {
+            shiny::textInput(inputId = inputId,
+                             label = label,
+                             value = "")
+        } else {
+            message('Why is this happening so much?')
+            shiny::textInput(inputId = inputId,
+                             label = label,
+                             value = currFn)
+        }
+    }
+    
+}
+
+rv_conf2conf <- function(rv) {
+    x <- shiny::reactiveValuesToList(rv$conf)
+    x$compounds<-shiny::reactiveValuesToList(rv$conf$compounds)
+    x
+}
+
+conf2rv_conf <- function(conf,rv) {
+    rv$conf <- shiny::reactiveValues(project=conf$project,
+                                     data=conf$data,
+                                     compounds=shiny::reactiveValues(known=conf$compounds$known,
+                                                                     unknown=conf$compounds$unknown,
+                                                                     setid=conf$compounds$setid))
+    rv
+    
+}

R/shiny-ui-config.R

+## Copyright (C) 2020 by University of Luxembourg
+
+## Licensed under the Apache License, Version 2.0 (the "License");
+## you may not use this file except in compliance with the License.
+## You may obtain a copy of the License at
+
+##     http://www.apache.org/licenses/LICENSE-2.0
+
+## Unless required by applicable law or agreed to in writing, software
+## distributed under the License is distributed on an "AS IS" BASIS,
+## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+## See the License for the specific language governing permissions and
+## limitations under the License.
+
+## Commentary:
+##
+## Defines config tab.
+
+mk_ui_config <- function() {
+    browseFile <- function(title,
+                           buttonName,
+                           txtName,
+                           buttonTxt="Import compound list.",
+                           txtTxt="",
+                           icon="file",
+                           description=NULL,
+                           ...) {
+        prim_box(title=title,
+                 shiny::h5(description),
+                 collapsible=F,...)}
+    
+    confImport <- prim_box(title="Import",
+                           shiny::uiOutput("fnKnownLCtrl"),
+                           shiny::uiOutput("fnUnkLCtrl"),
+                           shiny::uiOutput("fnSetIdCtrl"),
+                           shinyFiles::shinyFilesButton("impKnownListB",
+                                                        label="Import knowns.",
+                                                        title="",
+                                                        icon=shiny::icon("file"),
+                                                        multiple=F),
+                           shinyFiles::shinyFilesButton("impUnkListB",
+                                                        label="Import unknowns.",
+                                                        title="",
+                                                        icon=shiny::icon("file"),
+                                                        multiple=F),
+                           shinyFiles::shinyFilesButton("impSetIdB",
+                                                        label="Import set ID table.",
+                                                        title="",
+                                                        icon=shiny::icon("file"),
+                                                        multiple=T),
+                           width=NULL)
+
+    confmzMLTags <- prim_box(title="Tags",
+                             shiny::textInput("tagPropInp",
+                                              "What is a tag? (optional)",
+                                              value=TAG_DEF_DESC),
+                             shiny::textInput("tagsInp",
+                                              "Comma-delimited list of tag types.",
+                                              value=""),
+                             shiny::actionButton("updTagsB",
+                                                 label = "Update tags.",
+                                                 icon=shiny::icon("bomb")),
+
+                             width=NULL)
+
+    confState <- prim_box(title="Configuration State",
+                          shinyFiles::shinySaveButton("saveConfB",
+                                                      "Save configuration.",
+                                                      title="Save",
+                                                      filename = "conf-state.yaml",
+                                                      "yaml"),
+                          shinyFiles::shinyFilesButton("restoreConfB",
+                                                       label="Restore configuration.",
+                                                       multiple=F,
+                                                       title="Restore"),
+                          shiny::actionButton(inputId="resetConfB",
+                                              label="Reset config (CAUTION!)",
+                                              icon=shiny::icon("trash")),
+                          width=NULL)
+
+    confProj <- prim_box(title="Project",
+                         shinyFiles::shinyDirButton(id="switchProjB",
+                                                    label="Switch project.",
+                                                    title="Switch project.",
+                                                    icon=shiny::icon("recycle")),
+                         width=NULL)
+
+
+    confmzMLtab <-prim_box(title="Raw Files in mzML Format",
+                           shiny::h5("Use this file table to assign adduct modes and tags to the data files."),
+                           shinyFiles::shinyFilesButton("mzMLB",
+                                                        label="Select mzML files",
+                                                        title="Select mzML files",
+                                                        icon=shiny::icon("files-o"),
+                                                        multiple=T),
+                           rhandsontable::rHandsontableOutput("mzMLtabCtrl"),
+                           width=NULL)
+
+    
+    confLayout <- shiny::fluidRow(shiny::column(confImport,
+                                                confmzMLTags,
+                                                confState,
+                                                confProj,
+                                                width=4),
+                                  shiny::column(width=8,
+                                                confmzMLtab))
+
+
+    confTab <- shinydashboard::tabItem(tabName="config",
+                                       shiny::h2(GUI_TAB_TITLE[["conf"]]),
+                                       confLayout)
+
+    confSideItem <- shinydashboard::menuItem(text=GUI_SIDE_TITLE[["conf"]],
+                                             tabName="config",
+                                             icon=shiny::icon("user-cog"))
+
+    return(list(tab=confTab,
+                side=confSideItem))
+}
+
+react_conf_v <- function(input,output,session,rv,rf) {
+    rv$conf <- react_v(data=CONF$data,
+                       project=CONF$project,
+                       compounds=react_v(known=CONF$compounds$known,
+                                         unknown=CONF$compounds$unknown,
+                                         sets=CONF$compounds$sets))
+
+    rv
+}
+
+react_conf_f <- function(input,output,session,rv,rf) {
+    rf$get_proj_vol <- react_e(rv$conf$project,{
+        ## For shinyfiles dialogs.
+        path <- normalizePath(rv$conf$project, winslash = '/')
+        vls <- vols()() #Ugly! :)
+        vol <- path2vol(path)
+        sel<-match(vol,vls)
+        validate(sel,msg="Yikes! Unable to detect current project's volume.")
+        res<-names(vls)[[sel]]
+        res
+    })
+
+    rf$get_proj_path <- react_e(rv$conf$project,{
+        ## For shinyfiles dialogs.
+        wd <- rv$conf$project
+        vol <- rf$get_proj_vol()
+        v <- vols()()
+        pref<-v[[vol]]
+        res<-wd 
+        message('Relative project path is: ',res)
+        res
+    })
+    
+    rf
+}
+
+server_conf <- function(input,output,session,rv,rf) {
+    ## ***** shinyFiles observers *****
+    droot <- rf$get_proj_vol
+    dpath <- rf$get_proj_path
+    vs <- vols()
+    shinyFiles::shinyFileChoose(input, 'impKnownListB',defaultRoot=droot(),
+                                defaultPath=dpath(),roots=vs)
+    shinyFiles::shinyFileChoose(input, 'impUnkListB',defaultRoot=droot(),
+                                defaultPath=dpath(),roots=vs)
+    shinyFiles::shinyFileChoose(input, 'impSetIdB',defaultRoot=droot(),
+                                defaultPath=dpath(),roots=vs)
+    
+    shinyFiles::shinyFileSave(input, 'saveConfB',defaultRoot=droot(),
+                              defaultPath=dpath(),roots=vs)
+    shinyFiles::shinyFileChoose(input, 'restoreConfB',defaultRoot=droot(),
+                                defaultPath=dpath(),roots=vs)
+    shinyFiles::shinyFileChoose(input, 'mzMLB',defaultRoot=droot(),
+                                defaultPath=dpath(),roots=vs)
+    shinyFiles::shinyDirChoose(input, 'switchProjB',roots=vs)
+
+    obsrv_e(input$saveConfB, {
+        conf<-rv_conf2conf(rv)
+        vol <- vol_f()
+        fn <- shinyFiles::parseSavePath(roots=vol_f,input$saveConfB)[["datapath"]]
+        validate(fn,msg="Invalid file to save config to.")
+        write_conf(conf,fn)
+    })
+
+    obsrv_e(input$restoreConfB,{
+        fn <- shinyFiles::parseSavePath(roots=vol_f,input$saveConfB)[["datapath"]]
+        validate(fn,msg="Something went wrong with the config file name.")
+        validate(file.exists(fn),msg="The file is unreadable.")
+        conf <- read_conf(fn)
+        rv <- vonf2rv_conf(conf,rv)
+        
+    })
+    
+
+    obsrv_e(rv$conf,message("updated rv"))
+  
+    rv
+}

R/shiny-ui-top.R

+## Copyright (C) 2020 by University of Luxembourg
+
+## Licensed under the Apache License, Version 2.0 (the "License");
+## you may not use this file except in compliance with the License.
+## You may obtain a copy of the License at
+
+##     http://www.apache.org/licenses/LICENSE-2.0
+
+## Unless required by applicable law or agreed to in writing, software
+## distributed under the License is distributed on an "AS IS" BASIS,
+## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+## See the License for the specific language governing permissions and
+## limitations under the License. 
+
+## Commentary:
+##
+## This is a top-level Shiny file to bind them all.
+
+mk_ui <- function (fn_style) {
+    ## Top-level UI function.
+
+    headerText <- "Shinyscreen"
+    header <- shinydashboard::dashboardHeader(title=headerText,
+                                              shinydashboard::dropdownMenuOutput("notify"))
+
+
+    ## Plugins
+    conf <- mk_ui_config()
+    
+    sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(id='tabs',
+                                                                            conf$side,
+                                                                            shiny::hr(),
+                                                                            shiny::h5("Inputs"),
+                                                                            shiny::hr()))
+    body <- shinydashboard::dashboardBody(
+                                shiny::tags$head(shiny::tags$style(shiny::includeHTML(fn_style))),
+                                shinydashboard::tabItems(conf$tab))
+
+    shinydashboard::dashboardPage(
+                        header,
+                        sidebar,
+                        body)
+
+}
+
+mk_shinyscreen <- function(fn_style=system.file('www/custom.css',package = 'shinyscreen')) {
+    server <- function(input,output,session) {
+        ## Top-level server function.
+        rv <- shiny::reactiveValues(dummy=1) # Container for all
+                                             # reactive values.
+
+        rf <- list()                         # Container for all
+                                             # reactive functions.
+        
+        rv <- react_conf_v(input,output,session,rv=rv,rf=rf) # Config related r. values.
+        rf <- react_conf_f(input,output,session,rv=rv,rf=rf) # Config related r. functions.
+
+        ## Observers and renderers.
+        rv <- server_conf(input,output,session,rv=rv,rf=rf)
+        session$onSessionEnded(function () {
+            stopApp()
+        })
+    }
+    shiny::shinyApp(ui=mk_ui(fn_style=fn_style),server=server)
+
+}
+
+
+##' @export
+launch <- function(GUI=T,fn_conf="",...) {
+    if (GUI) {
+        app<-mk_shinyscreen()
+        shiny::runApp(appDir = app,...)
+    } else {
+        if (nchar(fnConf)==0) {
+            fn_conf <- commandArgs(trailingOnly=T)[[1]]
+        }
+        run(fn_conf)
+    }
+}

README.org

@@ -253,12 +253,37 @@
    In addition, the IDs of compounds belonging to the same set/mode
    combination must be unique. Different ID sets may overlap.
 
+   Essentially, sets serve the purpouse of visually grouping files in
+   the plots. Also, set combines those groups of files with particular
+   collections of compounds (from the compound set CSV file).
+
 ** Config Screen
    This is the start tab. Import the compound and set lists first,
    then proceed to import the mzML files. Provide tags in the tag text
    box and then assign the sets, modes and tags to the imported mzML
    files using table widget. Once this is done, move on to the
-   `Spectra Extraction' tab.
+   ~Spectra Extraction~ tab.
+
+*** Resetting State
+    In case some inputs have been changed, but the program for some
+    reason does not seem to respond to those changes, perhaps
+    resetting the state using the button ~Reset State~ will help. This
+    will clean the current compound state tables (but, all the inputs
+    remain unchanged).
+
+*** Switching Projects
+    The ~Switch project.~ button can be used to start new projects, or
+    change between them in the middle of processing.  
+
+    Switching projects while the program is running makes most sense
+    if it is desired to change some of the inputs (e.g. different set
+    configuration, or same compound lists but different files) while
+    retaining the others. The user is presented with a directory
+    change dialogue which is then used to select the new project
+    directory. If needed, a new project directory can be created from
+    the same dialogue. All the inputs that currently exist on the
+    configuration tab will be kept during switching. This way, only
+    what needs to be changed can be changed.
 
 ** Spectra Extraction
    Set the extraction parameters and then select a certain number of

man/RMB_EIC_prescreen_df.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{RMB_EIC_prescreen_df}
-\alias{RMB_EIC_prescreen_df}
-\title{Prescreen}
-\usage{
-RMB_EIC_prescreen_df(wd, RMB_mode, FileList, cmpd_list,
-  ppm_limit_fine = 10, EIC_limit = 0.001)
-}
-\arguments{
-\item{wd}{Absolute path to the directory that will contain the
-resulting data frame.}
-
-\item{RMB_mode}{...}
-
-\item{FileList}{...}
-
-\item{cmpd_list}{...}
-
-\item{ppm_limit_fine}{...}
-
-\item{EIC_limit}{...}
-}
-\description{
-Prescreens. Writes data out. Adapted from ReSOLUTION
-}
-\author{
-Emma Schymanski, Todor Kondić
-}

man/gen_cmpd_l.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{gen_cmpd_l}
-\alias{gen_cmpd_l}
-\title{Generate Compound List File}
-\usage{
-gen_cmpd_l(src_fn, dest_fn)
-}
-\arguments{
-\item{src_fn}{The input compound list CSV filename.}
-
-\item{dest_fn}{The resulting compound list CSV filename.}
-}
-\value{
-Number of compounds.
-}
-\description{
-Generate the RMassBank compound list from the input compound list
-in CSV file src_fn. The input compound list format is either a
-Chemical Dashboard csv file with, at least, PREFERRED_ SMILES
-columns \emph{filled} out, or just an ordinary CSV file with columns
-SMILES and Names filled. Argument dest_fn is the destination
-filename. Returns the number of compounds.
-}
-\author{
-Todor Kondić
-}

man/gen_cmpdl_and_load.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{gen_cmpdl_and_load}
-\alias{gen_cmpdl_and_load}
-\title{Generate and Load the RMassBank Compound List}
-\usage{
-gen_cmpdl_and_load(wd, fn_cmpdl)
-}
-\arguments{
-\item{wd}{Directory under which results are archived.}
-
-\item{fn_cmpdl}{The input compound list filename.}
-}
-\value{
-Named list. The key \code{fn_cmpdl} is the path of the
-generated compound list and the key \code{n} the number of
-compounds.
-}
-\description{
-Generates the RMassBank compound list and loads it.
-}
-\author{
-Todor Kondić
-}

man/gen_ftable.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{gen_ftable}
-\alias{gen_ftable}
-\title{Generate and Load the RMassBank Settings File}
-\usage{
-gen_ftable(fn_data, wd, n_cmpd)
-}
-\arguments{
-\item{fn_data}{The mzML filename.}
-
-\item{wd}{Directory under which results are archived.}
-
-\item{n_cmpd}{Number of compounds.}
-}
-\value{
-File path of the file table.
-}
-\description{
-Generates file table.
-}
-\author{
-Todor Kondić
-}

man/gen_stgs_and_load.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{gen_stgs_and_load}
-\alias{gen_stgs_and_load}
-\title{Generate and Load the RMassBank Settings File}
-\usage{
-gen_stgs_and_load(stgs, wd)
-}
-\arguments{
-\item{stgs}{Settings named list, or a settings filename.}
-
-\item{wd}{Directory under which results are archived.}
-}
-\value{
-result of RMassBank::loadRmbSettings
-}
-\description{
-Generates settings file and loads it.
-}
-\author{
-Todor Kondić
-}

man/mk_combine_file.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mk_combine_file}
-\alias{mk_combine_file}
-\title{Combine RMB Settings With Different Collisional Energies}
-\usage{
-mk_combine_file(sett_fns, fname)
-}
-\arguments{
-\item{sett_fns}{A list of settings files.}
-
-\item{fname}{The name of the combined file.}
-}
-\value{
-fname
-}
-\description{
-Combine the RMB settings files
-}
-\details{
-Combine RMB settings with different collisional energies into one
-settings file with multiple collisional energy entries.
-}
-\author{
-Todor Kondić
-}

man/mk_sett_file.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mk_sett_file}
-\alias{mk_sett_file}
-\title{Generate RMassBank settings file.}
-\usage{
-mk_sett_file(sett_alist, file)
-}
-\arguments{
-\item{sett_alist}{The named list of settings that are different
-from the RMassBank defaults.}
-
-\item{file}{The name of the YAML specification that will be merged
-with the template Rmb settings file.}
-}
-\description{
-Produce the Rmb Settings file
-}
-\details{
-Produce the Rmb Settings file based on the customisation file in
-YAML format.
-}

man/no_drama_mkdir.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{no_drama_mkdir}
-\alias{no_drama_mkdir}
-\title{Create directories without drama}
-\usage{
-no_drama_mkdir(path)
-}
-\arguments{
-\item{path}{Names of the directories.}
-}
-\value{
-The character string containing the input argument \code{path}.
-}
-\description{
-Create directories without drama.
-}
-\details{
-Create directories without drama.
-}
-\author{
-Todor Kondić
-}